Is there a correct orientation for the key in the ignition or is is preference? I ask because I keep getting it back from service the way I would consider to be wrong. Apparently someone there thinks it right or they think its funny to mess with customers.

It might be preference or laziness. Hard to say. If it's put in with the keychain on top of the key, you get a slight decrease in dangling keys and other junk people put on their keychains. That's about the only thing I can see as an advantage (if that's what you're considering the wrong way)